Hi I found that ive been having this issue alot lately at a number of datacentres, When they deply machines they have the issue the datacentres blame cpanel for this. As i have been told by others cpanel dose not ship a faulty rpm system its the images that these datacentres are using.

Your find that if you run the rm -rf /whatever for the rpm databases as detailed earlier

Then rebuild via WHM you should get it working but you may need to uninstall some rpm's basing on your needs etc.